Multiple sequence alignment - TraesCS7B01G143500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G143500 chr7B 100.000 4058 0 0 1 4058 184298362 184302419 0.000000e+00 7494.0
1 TraesCS7B01G143500 chr7B 87.079 178 21 2 1006 1183 683245403 683245578 2.470000e-47 200.0
2 TraesCS7B01G143500 chr7B 99.000 100 1 0 1713 1812 184299975 184300074 3.220000e-41 180.0
3 TraesCS7B01G143500 chr7B 99.000 100 1 0 1614 1713 184300074 184300173 3.220000e-41 180.0
4 TraesCS7B01G143500 chr7A 96.855 1717 46 5 1 1713 229144261 229142549 0.000000e+00 2865.0
5 TraesCS7B01G143500 chr7A 95.084 895 35 8 2780 3670 229141285 229140396 0.000000e+00 1400.0
6 TraesCS7B01G143500 chr7A 97.701 522 8 3 1713 2232 229142648 229142129 0.000000e+00 894.0
7 TraesCS7B01G143500 chr7A 91.573 534 22 7 2228 2738 229141826 229141293 0.000000e+00 715.0
8 TraesCS7B01G143500 chr7A 94.408 304 12 3 3668 3969 229138994 229138694 2.860000e-126 462.0
9 TraesCS7B01G143500 chr7A 90.588 85 2 3 3975 4058 229138518 229138439 1.540000e-19 108.0
10 TraesCS7B01G143500 chr7D 93.934 1698 63 12 2365 4036 216080738 216079055 0.000000e+00 2529.0
11 TraesCS7B01G143500 chr7D 96.420 1229 33 5 1 1221 216083335 216082110 0.000000e+00 2015.0
12 TraesCS7B01G143500 chr7D 97.108 657 12 5 1713 2367 216081461 216080810 0.000000e+00 1101.0
13 TraesCS7B01G143500 chr7D 93.789 483 24 4 1233 1713 216081840 216081362 0.000000e+00 721.0
14 TraesCS7B01G143500 chr5B 92.857 196 14 0 988 1183 450842129 450841934 6.640000e-73 285.0
15 TraesCS7B01G143500 chr5D 93.651 189 12 0 995 1183 377534597 377534409 2.390000e-72 283.0
16 TraesCS7B01G143500 chr5D 100.000 34 0 0 513 546 41876149 41876182 3.390000e-06 63.9
17 TraesCS7B01G143500 chr5A 93.651 189 12 0 995 1183 478322171 478321983 2.390000e-72 283.0
18 TraesCS7B01G143500 chr4B 87.640 178 20 2 1006 1183 149735483 149735658 5.320000e-49 206.0
19 TraesCS7B01G143500 chr6A 85.955 178 23 2 1006 1183 103975857 103975682 5.350000e-44 189.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G143500 chr7B 184298362 184302419 4057 False 2618.0 7494 99.333333 1 4058 3 chr7B.!!$F2 4057
1 TraesCS7B01G143500 chr7A 229138439 229144261 5822 True 1074.0 2865 94.368167 1 4058 6 chr7A.!!$R1 4057
2 TraesCS7B01G143500 chr7D 216079055 216083335 4280 True 1591.5 2529 95.312750 1 4036 4 chr7D.!!$R1 4035

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
896 908 0.810426 GAGGAATTCCGGCGTTCTCC 60.810 60.0 18.82 6.3 42.08 3.71 F
1639 1911 0.035458 GGTCCTCAGGTGGTCTTGTG 59.965 60.0 0.00 0.0 0.00 3.33 F
1731 2003 0.038744 AAGCATTGGTCCTCAGGTGG 59.961 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1991 0.035458 CACAAGACCACCTGAGGACC 59.965 60.000 4.99 0.0 0.00 4.46 R
2538 3204 0.674895 GACAATCTTCTGGTGCGCCT 60.675 55.000 18.96 0.0 35.27 5.52 R
3666 4357 1.339727 GCGGTCACTGGGGAAAGTTAT 60.340 52.381 0.00 0.0 0.00 1.89 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 3.056393 CCATGTGTTCATTGCTGGTGAAT 60.056 43.478 0.00 0.00 37.84 2.57
229 230 0.824759 GACTAATCAGGCGGGTCACT 59.175 55.000 0.00 0.00 0.00 3.41
829 840 2.202987 CCAGCTCATCCGCCTCAC 60.203 66.667 0.00 0.00 0.00 3.51
835 846 1.612146 TCATCCGCCTCACCCAAGA 60.612 57.895 0.00 0.00 0.00 3.02
836 847 1.153289 CATCCGCCTCACCCAAGAG 60.153 63.158 0.00 0.00 35.39 2.85
896 908 0.810426 GAGGAATTCCGGCGTTCTCC 60.810 60.000 18.82 6.30 42.08 3.71
1074 1086 2.264480 CTGGACGCGGACATCCAA 59.736 61.111 15.94 2.49 44.42 3.53
1210 1222 2.034124 CCCAAATCCGATTCATGGCTT 58.966 47.619 6.38 0.00 0.00 4.35
1212 1224 2.428171 CCAAATCCGATTCATGGCTTGT 59.572 45.455 0.00 0.00 0.00 3.16
1261 1531 1.521010 CTGCCACCTCTGATCAGCG 60.521 63.158 18.36 12.01 0.00 5.18
1379 1649 5.360999 TGACTCTTGATACTCCCACTGTATG 59.639 44.000 0.00 0.00 31.55 2.39
1440 1710 5.155509 TCGTGTCAATGTCTTTCAGTTTG 57.844 39.130 0.00 0.00 0.00 2.93
1463 1733 4.488126 TGTGATGTTAAACTGCAGAAGC 57.512 40.909 23.35 7.99 42.57 3.86
1498 1768 6.265577 AGATTATTGCTTGTTTTATGCCGTC 58.734 36.000 0.00 0.00 0.00 4.79
1636 1908 1.352352 CATTGGTCCTCAGGTGGTCTT 59.648 52.381 0.00 0.00 0.00 3.01
1637 1909 0.764890 TTGGTCCTCAGGTGGTCTTG 59.235 55.000 0.00 0.00 0.00 3.02
1638 1910 0.399949 TGGTCCTCAGGTGGTCTTGT 60.400 55.000 0.00 0.00 0.00 3.16
1639 1911 0.035458 GGTCCTCAGGTGGTCTTGTG 59.965 60.000 0.00 0.00 0.00 3.33
1640 1912 0.759346 GTCCTCAGGTGGTCTTGTGT 59.241 55.000 0.00 0.00 0.00 3.72
1641 1913 0.758734 TCCTCAGGTGGTCTTGTGTG 59.241 55.000 0.00 0.00 0.00 3.82
1642 1914 0.758734 CCTCAGGTGGTCTTGTGTGA 59.241 55.000 0.00 0.00 0.00 3.58
1643 1915 1.541233 CCTCAGGTGGTCTTGTGTGAC 60.541 57.143 0.00 0.00 36.31 3.67
1644 1916 1.414181 CTCAGGTGGTCTTGTGTGACT 59.586 52.381 0.00 0.00 37.16 3.41
1645 1917 2.628178 CTCAGGTGGTCTTGTGTGACTA 59.372 50.000 0.00 0.00 37.16 2.59
1646 1918 2.628178 TCAGGTGGTCTTGTGTGACTAG 59.372 50.000 0.00 0.00 37.16 2.57
1647 1919 2.628178 CAGGTGGTCTTGTGTGACTAGA 59.372 50.000 0.00 0.00 37.16 2.43
1648 1920 3.069586 CAGGTGGTCTTGTGTGACTAGAA 59.930 47.826 0.00 0.00 32.19 2.10
1649 1921 3.904339 AGGTGGTCTTGTGTGACTAGAAT 59.096 43.478 0.00 0.00 32.19 2.40
1650 1922 5.047306 CAGGTGGTCTTGTGTGACTAGAATA 60.047 44.000 0.00 0.00 32.19 1.75
1651 1923 5.186021 AGGTGGTCTTGTGTGACTAGAATAG 59.814 44.000 0.00 0.00 46.50 1.73
1652 1924 5.185249 GGTGGTCTTGTGTGACTAGAATAGA 59.815 44.000 0.00 0.00 42.77 1.98
1653 1925 6.326375 GTGGTCTTGTGTGACTAGAATAGAG 58.674 44.000 0.00 0.00 42.77 2.43
1654 1926 5.105716 TGGTCTTGTGTGACTAGAATAGAGC 60.106 44.000 0.00 0.00 42.77 4.09
1655 1927 5.105716 GGTCTTGTGTGACTAGAATAGAGCA 60.106 44.000 0.00 0.00 42.77 4.26
1656 1928 6.406400 GGTCTTGTGTGACTAGAATAGAGCAT 60.406 42.308 0.00 0.00 42.77 3.79
1657 1929 7.201830 GGTCTTGTGTGACTAGAATAGAGCATA 60.202 40.741 0.00 0.00 42.77 3.14
1658 1930 7.646130 GTCTTGTGTGACTAGAATAGAGCATAC 59.354 40.741 0.00 0.00 42.77 2.39
1659 1931 6.392625 TGTGTGACTAGAATAGAGCATACC 57.607 41.667 0.00 0.00 42.77 2.73
1660 1932 5.891551 TGTGTGACTAGAATAGAGCATACCA 59.108 40.000 0.00 0.00 42.77 3.25
1661 1933 6.039829 TGTGTGACTAGAATAGAGCATACCAG 59.960 42.308 0.00 0.00 42.77 4.00
1662 1934 6.263392 GTGTGACTAGAATAGAGCATACCAGA 59.737 42.308 0.00 0.00 42.77 3.86
1663 1935 6.263392 TGTGACTAGAATAGAGCATACCAGAC 59.737 42.308 0.00 0.00 42.77 3.51
1664 1936 6.488683 GTGACTAGAATAGAGCATACCAGACT 59.511 42.308 0.00 0.00 42.77 3.24
1665 1937 7.662258 GTGACTAGAATAGAGCATACCAGACTA 59.338 40.741 0.00 0.00 42.77 2.59
1666 1938 7.880713 TGACTAGAATAGAGCATACCAGACTAG 59.119 40.741 0.00 0.00 42.77 2.57
1667 1939 5.975693 AGAATAGAGCATACCAGACTAGC 57.024 43.478 0.00 0.00 0.00 3.42
1668 1940 5.389520 AGAATAGAGCATACCAGACTAGCA 58.610 41.667 0.00 0.00 0.00 3.49
1669 1941 6.015918 AGAATAGAGCATACCAGACTAGCAT 58.984 40.000 0.00 0.00 0.00 3.79
1670 1942 6.496565 AGAATAGAGCATACCAGACTAGCATT 59.503 38.462 0.00 0.00 0.00 3.56
1671 1943 4.599047 AGAGCATACCAGACTAGCATTC 57.401 45.455 0.00 0.00 0.00 2.67
1672 1944 4.222336 AGAGCATACCAGACTAGCATTCT 58.778 43.478 0.00 0.00 0.00 2.40
1673 1945 4.653341 AGAGCATACCAGACTAGCATTCTT 59.347 41.667 0.00 0.00 0.00 2.52
1674 1946 5.130145 AGAGCATACCAGACTAGCATTCTTT 59.870 40.000 0.00 0.00 0.00 2.52
1675 1947 5.121811 AGCATACCAGACTAGCATTCTTTG 58.878 41.667 0.00 0.00 0.00 2.77
1676 1948 4.878397 GCATACCAGACTAGCATTCTTTGT 59.122 41.667 0.00 0.00 0.00 2.83
1677 1949 5.220739 GCATACCAGACTAGCATTCTTTGTG 60.221 44.000 0.00 0.00 0.00 3.33
1678 1950 3.077359 ACCAGACTAGCATTCTTTGTGC 58.923 45.455 0.00 0.00 42.81 4.57
1687 1959 4.488126 GCATTCTTTGTGCTACAAGTCA 57.512 40.909 0.00 0.00 39.53 3.41
1688 1960 5.051891 GCATTCTTTGTGCTACAAGTCAT 57.948 39.130 0.00 0.00 39.53 3.06
1689 1961 4.855388 GCATTCTTTGTGCTACAAGTCATG 59.145 41.667 0.00 0.00 39.53 3.07
1690 1962 5.396484 CATTCTTTGTGCTACAAGTCATGG 58.604 41.667 0.00 0.00 39.53 3.66
1691 1963 4.085357 TCTTTGTGCTACAAGTCATGGT 57.915 40.909 0.00 0.00 39.53 3.55
1692 1964 4.460263 TCTTTGTGCTACAAGTCATGGTT 58.540 39.130 0.00 0.00 39.53 3.67
1693 1965 4.887071 TCTTTGTGCTACAAGTCATGGTTT 59.113 37.500 0.00 0.00 39.53 3.27
1694 1966 5.359576 TCTTTGTGCTACAAGTCATGGTTTT 59.640 36.000 0.00 0.00 39.53 2.43
1695 1967 4.829064 TGTGCTACAAGTCATGGTTTTC 57.171 40.909 0.00 0.00 0.00 2.29
1696 1968 3.568007 TGTGCTACAAGTCATGGTTTTCC 59.432 43.478 0.00 0.00 41.14 3.13
1697 1969 3.821033 GTGCTACAAGTCATGGTTTTCCT 59.179 43.478 0.00 0.00 41.38 3.36
1698 1970 4.278419 GTGCTACAAGTCATGGTTTTCCTT 59.722 41.667 0.00 0.00 41.38 3.36
1699 1971 4.892934 TGCTACAAGTCATGGTTTTCCTTT 59.107 37.500 0.00 0.00 41.38 3.11
1700 1972 5.362430 TGCTACAAGTCATGGTTTTCCTTTT 59.638 36.000 0.00 0.00 41.38 2.27
1701 1973 5.920840 GCTACAAGTCATGGTTTTCCTTTTC 59.079 40.000 0.00 0.00 41.38 2.29
1702 1974 6.239036 GCTACAAGTCATGGTTTTCCTTTTCT 60.239 38.462 0.00 0.00 41.38 2.52
1703 1975 5.906073 ACAAGTCATGGTTTTCCTTTTCTG 58.094 37.500 0.00 0.00 41.38 3.02
1704 1976 4.590850 AGTCATGGTTTTCCTTTTCTGC 57.409 40.909 0.00 0.00 41.38 4.26
1705 1977 4.218312 AGTCATGGTTTTCCTTTTCTGCT 58.782 39.130 0.00 0.00 41.38 4.24
1706 1978 4.038402 AGTCATGGTTTTCCTTTTCTGCTG 59.962 41.667 0.00 0.00 41.38 4.41
1707 1979 2.888834 TGGTTTTCCTTTTCTGCTGC 57.111 45.000 0.00 0.00 41.38 5.25
1708 1980 2.106566 TGGTTTTCCTTTTCTGCTGCA 58.893 42.857 0.88 0.88 41.38 4.41
1709 1981 2.699846 TGGTTTTCCTTTTCTGCTGCAT 59.300 40.909 1.31 0.00 41.38 3.96
1710 1982 3.062042 GGTTTTCCTTTTCTGCTGCATG 58.938 45.455 1.31 0.00 36.94 4.06
1711 1983 3.493176 GGTTTTCCTTTTCTGCTGCATGT 60.493 43.478 1.31 0.00 36.94 3.21
1712 1984 4.261994 GGTTTTCCTTTTCTGCTGCATGTA 60.262 41.667 1.31 0.00 36.94 2.29
1713 1985 5.288804 GTTTTCCTTTTCTGCTGCATGTAA 58.711 37.500 1.31 0.00 0.00 2.41
1714 1986 4.771590 TTCCTTTTCTGCTGCATGTAAG 57.228 40.909 1.31 6.78 0.00 2.34
1715 1987 2.489329 TCCTTTTCTGCTGCATGTAAGC 59.511 45.455 1.31 13.71 41.22 3.09
1721 1993 1.548081 TGCTGCATGTAAGCATTGGT 58.452 45.000 17.89 0.00 45.50 3.67
1722 1994 1.473677 TGCTGCATGTAAGCATTGGTC 59.526 47.619 17.89 0.00 45.50 4.02
1723 1995 1.202336 GCTGCATGTAAGCATTGGTCC 60.202 52.381 15.19 0.00 44.68 4.46
1724 1996 2.372264 CTGCATGTAAGCATTGGTCCT 58.628 47.619 0.00 0.00 44.68 3.85
1725 1997 2.357009 CTGCATGTAAGCATTGGTCCTC 59.643 50.000 0.00 0.00 44.68 3.71
1726 1998 2.290832 TGCATGTAAGCATTGGTCCTCA 60.291 45.455 0.00 0.00 40.11 3.86
1727 1999 2.357009 GCATGTAAGCATTGGTCCTCAG 59.643 50.000 0.00 0.00 31.99 3.35
1728 2000 2.787473 TGTAAGCATTGGTCCTCAGG 57.213 50.000 0.00 0.00 0.00 3.86
1729 2001 1.985159 TGTAAGCATTGGTCCTCAGGT 59.015 47.619 0.00 0.00 0.00 4.00
1730 2002 2.290260 TGTAAGCATTGGTCCTCAGGTG 60.290 50.000 0.00 0.00 0.00 4.00
1731 2003 0.038744 AAGCATTGGTCCTCAGGTGG 59.961 55.000 0.00 0.00 0.00 4.61
1732 2004 1.136329 AGCATTGGTCCTCAGGTGGT 61.136 55.000 0.00 0.00 0.00 4.16
1733 2005 0.678048 GCATTGGTCCTCAGGTGGTC 60.678 60.000 0.00 0.00 0.00 4.02
1734 2006 0.987294 CATTGGTCCTCAGGTGGTCT 59.013 55.000 0.00 0.00 0.00 3.85
1857 2129 9.529325 TTCGTATTGTCTAACTTCATTATCAGG 57.471 33.333 0.00 0.00 0.00 3.86
1874 2146 7.792374 TTATCAGGTTGTCAGATCTTTATGC 57.208 36.000 0.00 0.00 0.00 3.14
2032 2304 6.013206 TGGTCCTAGTTTTGGCAATACTCTAA 60.013 38.462 23.56 8.69 0.00 2.10
2214 2488 7.880160 TCCCATTTTTGGTACATAATCTCAG 57.120 36.000 0.00 0.00 39.30 3.35
2351 2936 2.430546 TGCCGTTATTGTTTTGGCTG 57.569 45.000 2.99 0.00 45.90 4.85
2367 3026 5.913137 TTGGCTGTTATTTTCCATGGTAG 57.087 39.130 12.58 0.42 0.00 3.18
2459 3118 8.557592 TGATATCATTATCTTGCTTGCTTAGG 57.442 34.615 0.00 0.00 36.07 2.69
2468 3127 0.961753 GCTTGCTTAGGTGGTGCTTT 59.038 50.000 0.00 0.00 0.00 3.51
2470 3129 2.224042 GCTTGCTTAGGTGGTGCTTTTT 60.224 45.455 0.00 0.00 0.00 1.94
2538 3204 7.155655 TGTAATCATAATGAACAGCTTTGCA 57.844 32.000 0.00 0.00 0.00 4.08
2622 3288 4.335315 TGAGCTCATGAAAGTTGAAACGTT 59.665 37.500 13.74 0.00 33.36 3.99
2745 3432 3.327757 TGCCAACAGACTAACTCAAGGAT 59.672 43.478 0.00 0.00 0.00 3.24
2750 3437 5.669164 ACAGACTAACTCAAGGATCCTTC 57.331 43.478 24.67 10.75 33.42 3.46
2751 3438 5.087323 ACAGACTAACTCAAGGATCCTTCA 58.913 41.667 24.67 11.57 33.42 3.02
2769 3456 5.068987 TCCTTCAGGTTTCAAACATTTCCTG 59.931 40.000 1.93 0.00 42.36 3.86
2771 3458 8.725190 TCCTTCAGGTTTCAAACATTTCCTGTT 61.725 37.037 1.93 0.00 42.21 3.16
2784 3471 7.296628 ACATTTCCTGTTGCCTTTAATGTTA 57.703 32.000 0.00 0.00 32.90 2.41
2785 3472 7.906327 ACATTTCCTGTTGCCTTTAATGTTAT 58.094 30.769 0.00 0.00 32.90 1.89
2786 3473 8.374743 ACATTTCCTGTTGCCTTTAATGTTATT 58.625 29.630 0.00 0.00 32.90 1.40
2787 3474 9.868277 CATTTCCTGTTGCCTTTAATGTTATTA 57.132 29.630 0.00 0.00 0.00 0.98
2791 3478 9.868277 TCCTGTTGCCTTTAATGTTATTATTTG 57.132 29.630 0.00 0.00 0.00 2.32
2792 3479 8.603181 CCTGTTGCCTTTAATGTTATTATTTGC 58.397 33.333 0.00 0.00 0.00 3.68
2793 3480 9.369904 CTGTTGCCTTTAATGTTATTATTTGCT 57.630 29.630 0.00 0.00 0.00 3.91
2794 3481 9.717942 TGTTGCCTTTAATGTTATTATTTGCTT 57.282 25.926 0.00 0.00 0.00 3.91
2796 3483 8.627487 TGCCTTTAATGTTATTATTTGCTTCG 57.373 30.769 0.00 0.00 0.00 3.79
2797 3484 8.247562 TGCCTTTAATGTTATTATTTGCTTCGT 58.752 29.630 0.00 0.00 0.00 3.85
2809 3496 2.673976 TGCTTCGTTTTCTTTACGGC 57.326 45.000 0.00 0.00 39.38 5.68
2825 3512 5.574891 TTACGGCATGTCATTATTGCTTT 57.425 34.783 0.00 0.00 36.62 3.51
2843 3530 6.088016 TGCTTTGTAGTTCATCATGCTTTT 57.912 33.333 0.00 0.00 0.00 2.27
2866 3553 3.636300 GGGACATTTAACATGGCATGCTA 59.364 43.478 26.70 16.70 0.00 3.49
2879 3566 2.620585 GGCATGCTACAATCCTCCTTTC 59.379 50.000 18.92 0.00 0.00 2.62
2895 3582 0.672889 TTTCGCAGGCTGAAATTGCA 59.327 45.000 20.86 0.00 37.69 4.08
3009 3696 1.280421 GGAGCCCTTGAGATCACAGTT 59.720 52.381 0.00 0.00 0.00 3.16
3079 3766 0.031111 TATGAGCTAGGGTGGCACCT 60.031 55.000 33.87 22.22 44.75 4.00
3429 4120 1.488393 GGGCTGGAGCTATCTGTTCTT 59.512 52.381 0.00 0.00 41.70 2.52
3430 4121 2.559440 GGCTGGAGCTATCTGTTCTTG 58.441 52.381 0.00 0.00 41.70 3.02
3431 4122 2.093235 GGCTGGAGCTATCTGTTCTTGT 60.093 50.000 0.00 0.00 41.70 3.16
3444 4135 4.282449 TCTGTTCTTGTCCCAGTCGATAAA 59.718 41.667 0.00 0.00 0.00 1.40
3490 4181 4.199432 AGATTCAGTTGTGCTCCTACAG 57.801 45.455 0.00 0.00 0.00 2.74
3502 4193 9.341899 GTTGTGCTCCTACAGTTTAATTATTTG 57.658 33.333 0.00 0.00 0.00 2.32
3505 4196 8.026607 GTGCTCCTACAGTTTAATTATTTGCAA 58.973 33.333 0.00 0.00 0.00 4.08
3580 4271 1.901464 GCACGGGGTCACCATGTTT 60.901 57.895 0.00 0.00 40.22 2.83
3628 4319 4.938226 GGTCAACCTAATGAGAAGTCAAGG 59.062 45.833 0.00 0.00 36.91 3.61
3631 4322 4.213564 ACCTAATGAGAAGTCAAGGCTG 57.786 45.455 0.00 0.00 34.96 4.85
3666 4357 1.776969 TGAGGCTCAGAGTGGGAGA 59.223 57.895 14.43 0.00 34.24 3.71
3670 5765 2.364002 GAGGCTCAGAGTGGGAGATAAC 59.636 54.545 10.25 0.00 34.24 1.89
3749 5844 3.737355 GCTCCTGATAACGACTGTTACCC 60.737 52.174 0.00 0.00 43.03 3.69
3932 6029 8.486210 AGTAATAAATACAGTCCTGAGAATGCA 58.514 33.333 0.40 0.00 41.83 3.96
4039 6307 9.802039 TTGGCTAACCTTATTTATATTAGGTGG 57.198 33.333 4.86 3.51 41.68 4.61
4040 6308 9.173231 TGGCTAACCTTATTTATATTAGGTGGA 57.827 33.333 4.86 0.00 41.68 4.02
4041 6309 9.668497 GGCTAACCTTATTTATATTAGGTGGAG 57.332 37.037 4.86 6.82 41.68 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 2.364186 TCGATCCAGCTGAGCCCA 60.364 61.111 17.39 0.00 0.00 5.36
167 168 0.890542 GCTGAGCATGGGTGTGACAA 60.891 55.000 0.00 0.00 0.00 3.18
829 840 2.256461 GCTTTGCGTGCTCTTGGG 59.744 61.111 0.00 0.00 0.00 4.12
835 846 2.331451 GTTTCGGCTTTGCGTGCT 59.669 55.556 0.00 0.00 0.00 4.40
836 847 2.010817 CTGTTTCGGCTTTGCGTGC 61.011 57.895 0.00 0.00 0.00 5.34
892 904 0.753479 CTAGGGCTTGCGAGAGGAGA 60.753 60.000 4.70 0.00 0.00 3.71
896 908 0.529555 GCTTCTAGGGCTTGCGAGAG 60.530 60.000 4.70 0.00 0.00 3.20
1074 1086 2.362503 TCCCTCATGACGCGGTCT 60.363 61.111 12.47 0.00 33.15 3.85
1187 1199 1.411501 CCATGAATCGGATTTGGGGGT 60.412 52.381 11.90 0.00 0.00 4.95
1188 1200 1.331214 CCATGAATCGGATTTGGGGG 58.669 55.000 11.90 5.71 0.00 5.40
1251 1521 1.205417 TGATGCAGAACGCTGATCAGA 59.795 47.619 27.04 2.72 45.17 3.27
1397 1667 5.146460 CGAAATCATCAAGAAAAACTCGCA 58.854 37.500 0.00 0.00 0.00 5.10
1440 1710 4.676924 GCTTCTGCAGTTTAACATCACAAC 59.323 41.667 14.67 0.00 39.41 3.32
1463 1733 9.630098 AAACAAGCAATAATCTCTTACATTGTG 57.370 29.630 0.00 0.00 32.25 3.33
1498 1768 0.806102 CTGACGCCCTTGTGGATACG 60.806 60.000 0.00 0.00 42.51 3.06
1636 1908 5.891551 TGGTATGCTCTATTCTAGTCACACA 59.108 40.000 0.00 0.00 0.00 3.72
1637 1909 6.263392 TCTGGTATGCTCTATTCTAGTCACAC 59.737 42.308 0.00 0.00 0.00 3.82
1638 1910 6.263392 GTCTGGTATGCTCTATTCTAGTCACA 59.737 42.308 0.00 0.00 0.00 3.58
1639 1911 6.488683 AGTCTGGTATGCTCTATTCTAGTCAC 59.511 42.308 0.00 0.00 0.00 3.67
1640 1912 6.606069 AGTCTGGTATGCTCTATTCTAGTCA 58.394 40.000 0.00 0.00 0.00 3.41
1641 1913 7.148306 GCTAGTCTGGTATGCTCTATTCTAGTC 60.148 44.444 0.00 0.00 0.00 2.59
1642 1914 6.657541 GCTAGTCTGGTATGCTCTATTCTAGT 59.342 42.308 0.00 0.00 0.00 2.57
1643 1915 6.657117 TGCTAGTCTGGTATGCTCTATTCTAG 59.343 42.308 0.00 0.00 0.00 2.43
1644 1916 6.543735 TGCTAGTCTGGTATGCTCTATTCTA 58.456 40.000 0.00 0.00 0.00 2.10
1645 1917 5.389520 TGCTAGTCTGGTATGCTCTATTCT 58.610 41.667 0.00 0.00 0.00 2.40
1646 1918 5.713792 TGCTAGTCTGGTATGCTCTATTC 57.286 43.478 0.00 0.00 0.00 1.75
1647 1919 6.496565 AGAATGCTAGTCTGGTATGCTCTATT 59.503 38.462 0.00 0.00 0.00 1.73
1648 1920 6.015918 AGAATGCTAGTCTGGTATGCTCTAT 58.984 40.000 0.00 0.00 0.00 1.98
1649 1921 5.389520 AGAATGCTAGTCTGGTATGCTCTA 58.610 41.667 0.00 0.00 0.00 2.43
1650 1922 4.222336 AGAATGCTAGTCTGGTATGCTCT 58.778 43.478 0.00 0.00 0.00 4.09
1651 1923 4.599047 AGAATGCTAGTCTGGTATGCTC 57.401 45.455 0.00 0.00 0.00 4.26
1652 1924 5.121811 CAAAGAATGCTAGTCTGGTATGCT 58.878 41.667 0.00 0.00 0.00 3.79
1653 1925 4.878397 ACAAAGAATGCTAGTCTGGTATGC 59.122 41.667 0.00 0.00 0.00 3.14
1654 1926 5.220739 GCACAAAGAATGCTAGTCTGGTATG 60.221 44.000 0.00 0.00 40.08 2.39
1655 1927 4.878397 GCACAAAGAATGCTAGTCTGGTAT 59.122 41.667 0.00 0.00 40.08 2.73
1656 1928 4.253685 GCACAAAGAATGCTAGTCTGGTA 58.746 43.478 0.00 0.00 40.08 3.25
1657 1929 3.077359 GCACAAAGAATGCTAGTCTGGT 58.923 45.455 0.00 0.00 40.08 4.00
1658 1930 3.754188 GCACAAAGAATGCTAGTCTGG 57.246 47.619 0.00 0.00 40.08 3.86
1666 1938 4.488126 TGACTTGTAGCACAAAGAATGC 57.512 40.909 3.84 0.00 37.69 3.56
1667 1939 5.048504 ACCATGACTTGTAGCACAAAGAATG 60.049 40.000 0.00 6.76 37.69 2.67
1668 1940 5.072741 ACCATGACTTGTAGCACAAAGAAT 58.927 37.500 0.00 0.00 37.69 2.40
1669 1941 4.460263 ACCATGACTTGTAGCACAAAGAA 58.540 39.130 0.00 0.00 37.69 2.52
1670 1942 4.085357 ACCATGACTTGTAGCACAAAGA 57.915 40.909 0.00 0.00 37.69 2.52
1671 1943 4.836125 AACCATGACTTGTAGCACAAAG 57.164 40.909 0.00 0.00 37.69 2.77
1672 1944 5.451242 GGAAAACCATGACTTGTAGCACAAA 60.451 40.000 0.00 0.00 37.69 2.83
1673 1945 4.037446 GGAAAACCATGACTTGTAGCACAA 59.963 41.667 0.00 2.49 36.54 3.33
1674 1946 3.568007 GGAAAACCATGACTTGTAGCACA 59.432 43.478 0.00 0.00 0.00 4.57
1675 1947 3.821033 AGGAAAACCATGACTTGTAGCAC 59.179 43.478 0.00 0.00 0.00 4.40
1676 1948 4.098914 AGGAAAACCATGACTTGTAGCA 57.901 40.909 0.00 0.00 0.00 3.49
1677 1949 5.453567 AAAGGAAAACCATGACTTGTAGC 57.546 39.130 0.00 0.00 0.00 3.58
1678 1950 7.141363 CAGAAAAGGAAAACCATGACTTGTAG 58.859 38.462 0.00 0.00 0.00 2.74
1679 1951 6.460953 GCAGAAAAGGAAAACCATGACTTGTA 60.461 38.462 0.00 0.00 0.00 2.41
1680 1952 5.682212 GCAGAAAAGGAAAACCATGACTTGT 60.682 40.000 0.00 0.00 0.00 3.16
1681 1953 4.746611 GCAGAAAAGGAAAACCATGACTTG 59.253 41.667 0.00 0.00 0.00 3.16
1682 1954 4.651045 AGCAGAAAAGGAAAACCATGACTT 59.349 37.500 0.00 0.00 0.00 3.01
1683 1955 4.038402 CAGCAGAAAAGGAAAACCATGACT 59.962 41.667 0.00 0.00 0.00 3.41
1684 1956 4.301628 CAGCAGAAAAGGAAAACCATGAC 58.698 43.478 0.00 0.00 0.00 3.06
1685 1957 3.243839 GCAGCAGAAAAGGAAAACCATGA 60.244 43.478 0.00 0.00 0.00 3.07
1686 1958 3.062042 GCAGCAGAAAAGGAAAACCATG 58.938 45.455 0.00 0.00 0.00 3.66
1687 1959 2.699846 TGCAGCAGAAAAGGAAAACCAT 59.300 40.909 0.00 0.00 0.00 3.55
1688 1960 2.106566 TGCAGCAGAAAAGGAAAACCA 58.893 42.857 0.00 0.00 0.00 3.67
1689 1961 2.888834 TGCAGCAGAAAAGGAAAACC 57.111 45.000 0.00 0.00 0.00 3.27
1690 1962 3.721035 ACATGCAGCAGAAAAGGAAAAC 58.279 40.909 0.00 0.00 0.00 2.43
1691 1963 5.528043 TTACATGCAGCAGAAAAGGAAAA 57.472 34.783 0.00 0.00 0.00 2.29
1692 1964 4.559300 GCTTACATGCAGCAGAAAAGGAAA 60.559 41.667 11.73 0.00 37.22 3.13
1693 1965 3.057315 GCTTACATGCAGCAGAAAAGGAA 60.057 43.478 11.73 0.00 37.22 3.36
1694 1966 2.489329 GCTTACATGCAGCAGAAAAGGA 59.511 45.455 11.73 0.00 37.22 3.36
1695 1967 2.229543 TGCTTACATGCAGCAGAAAAGG 59.770 45.455 14.69 0.00 42.49 3.11
1696 1968 3.564235 TGCTTACATGCAGCAGAAAAG 57.436 42.857 14.69 5.20 42.49 2.27
1703 1975 1.202336 GGACCAATGCTTACATGCAGC 60.202 52.381 10.03 10.03 46.71 5.25
1704 1976 2.357009 GAGGACCAATGCTTACATGCAG 59.643 50.000 0.00 0.00 46.71 4.41
1706 1978 2.357009 CTGAGGACCAATGCTTACATGC 59.643 50.000 0.00 0.00 36.36 4.06
1707 1979 2.947652 CCTGAGGACCAATGCTTACATG 59.052 50.000 0.00 0.00 36.36 3.21
1708 1980 2.578021 ACCTGAGGACCAATGCTTACAT 59.422 45.455 4.99 0.00 38.49 2.29
1709 1981 1.985159 ACCTGAGGACCAATGCTTACA 59.015 47.619 4.99 0.00 0.00 2.41
1710 1982 2.359900 CACCTGAGGACCAATGCTTAC 58.640 52.381 4.99 0.00 0.00 2.34
1711 1983 1.281867 CCACCTGAGGACCAATGCTTA 59.718 52.381 4.99 0.00 0.00 3.09
1712 1984 0.038744 CCACCTGAGGACCAATGCTT 59.961 55.000 4.99 0.00 0.00 3.91
1713 1985 1.136329 ACCACCTGAGGACCAATGCT 61.136 55.000 4.99 0.00 0.00 3.79
1714 1986 0.678048 GACCACCTGAGGACCAATGC 60.678 60.000 4.99 0.00 0.00 3.56
1715 1987 0.987294 AGACCACCTGAGGACCAATG 59.013 55.000 4.99 0.00 0.00 2.82
1716 1988 1.352352 CAAGACCACCTGAGGACCAAT 59.648 52.381 4.99 0.00 0.00 3.16
1717 1989 0.764890 CAAGACCACCTGAGGACCAA 59.235 55.000 4.99 0.00 0.00 3.67
1718 1990 0.399949 ACAAGACCACCTGAGGACCA 60.400 55.000 4.99 0.00 0.00 4.02
1719 1991 0.035458 CACAAGACCACCTGAGGACC 59.965 60.000 4.99 0.00 0.00 4.46
1720 1992 0.759346 ACACAAGACCACCTGAGGAC 59.241 55.000 4.99 0.00 0.00 3.85
1721 1993 0.758734 CACACAAGACCACCTGAGGA 59.241 55.000 4.99 0.00 0.00 3.71
1722 1994 0.758734 TCACACAAGACCACCTGAGG 59.241 55.000 0.00 0.00 0.00 3.86
1723 1995 1.414181 AGTCACACAAGACCACCTGAG 59.586 52.381 0.00 0.00 39.34 3.35
1724 1996 1.496060 AGTCACACAAGACCACCTGA 58.504 50.000 0.00 0.00 39.34 3.86
1725 1997 2.628178 TCTAGTCACACAAGACCACCTG 59.372 50.000 0.00 0.00 39.34 4.00
1726 1998 2.958818 TCTAGTCACACAAGACCACCT 58.041 47.619 0.00 0.00 39.34 4.00
1727 1999 3.746045 TTCTAGTCACACAAGACCACC 57.254 47.619 0.00 0.00 39.34 4.61
1728 2000 6.268825 TCTATTCTAGTCACACAAGACCAC 57.731 41.667 0.00 0.00 39.34 4.16
1729 2001 5.105716 GCTCTATTCTAGTCACACAAGACCA 60.106 44.000 0.00 0.00 39.34 4.02
1730 2002 5.105716 TGCTCTATTCTAGTCACACAAGACC 60.106 44.000 0.00 0.00 39.34 3.85
1731 2003 5.955488 TGCTCTATTCTAGTCACACAAGAC 58.045 41.667 0.00 0.00 38.81 3.01
1732 2004 6.782082 ATGCTCTATTCTAGTCACACAAGA 57.218 37.500 0.00 0.00 0.00 3.02
1733 2005 8.355913 TGATATGCTCTATTCTAGTCACACAAG 58.644 37.037 0.00 0.00 0.00 3.16
1734 2006 8.237811 TGATATGCTCTATTCTAGTCACACAA 57.762 34.615 0.00 0.00 0.00 3.33
1857 2129 5.091431 GCACAAGCATAAAGATCTGACAAC 58.909 41.667 0.00 0.00 41.58 3.32
1874 2146 9.935682 CTAAGTAACCATATTTACATGCACAAG 57.064 33.333 0.00 0.00 34.83 3.16
2214 2488 5.411781 CAACTGTTAGGGTGTATGAGTCTC 58.588 45.833 0.00 0.00 0.00 3.36
2245 2830 4.336889 AACTGGTCAGATTCACGAAGAA 57.663 40.909 4.84 0.00 41.28 2.52
2351 2936 8.827677 CACTTACTAGCTACCATGGAAAATAAC 58.172 37.037 21.47 0.00 0.00 1.89
2367 3026 5.277538 GCATCTTATGTTGGCACTTACTAGC 60.278 44.000 0.00 0.00 0.00 3.42
2459 3118 6.526674 CGGATACTTAATTGAAAAAGCACCAC 59.473 38.462 0.00 0.00 0.00 4.16
2538 3204 0.674895 GACAATCTTCTGGTGCGCCT 60.675 55.000 18.96 0.00 35.27 5.52
2622 3288 4.080807 TGTTAGTTTGAAGACCTCACCACA 60.081 41.667 0.00 0.00 32.21 4.17
2715 3402 4.999950 AGTTAGTCTGTTGGCATCTTTCAG 59.000 41.667 0.00 0.00 0.00 3.02
2716 3403 4.973168 AGTTAGTCTGTTGGCATCTTTCA 58.027 39.130 0.00 0.00 0.00 2.69
2745 3432 5.068987 CAGGAAATGTTTGAAACCTGAAGGA 59.931 40.000 5.50 0.00 45.02 3.36
2771 3458 8.247562 ACGAAGCAAATAATAACATTAAAGGCA 58.752 29.630 0.00 0.00 0.00 4.75
2772 3459 8.628882 ACGAAGCAAATAATAACATTAAAGGC 57.371 30.769 0.00 0.00 0.00 4.35
2784 3471 6.307077 GCCGTAAAGAAAACGAAGCAAATAAT 59.693 34.615 0.00 0.00 42.90 1.28
2785 3472 5.626132 GCCGTAAAGAAAACGAAGCAAATAA 59.374 36.000 0.00 0.00 42.90 1.40
2786 3473 5.148568 GCCGTAAAGAAAACGAAGCAAATA 58.851 37.500 0.00 0.00 42.90 1.40
2787 3474 3.978855 GCCGTAAAGAAAACGAAGCAAAT 59.021 39.130 0.00 0.00 42.90 2.32
2788 3475 3.181499 TGCCGTAAAGAAAACGAAGCAAA 60.181 39.130 0.00 0.00 42.90 3.68
2789 3476 2.355132 TGCCGTAAAGAAAACGAAGCAA 59.645 40.909 0.00 0.00 42.90 3.91
2790 3477 1.941294 TGCCGTAAAGAAAACGAAGCA 59.059 42.857 0.00 0.00 42.90 3.91
2791 3478 2.673976 TGCCGTAAAGAAAACGAAGC 57.326 45.000 0.00 0.00 42.90 3.86
2792 3479 4.141855 ACATGCCGTAAAGAAAACGAAG 57.858 40.909 0.00 0.00 42.90 3.79
2793 3480 3.560481 TGACATGCCGTAAAGAAAACGAA 59.440 39.130 0.00 0.00 42.90 3.85
2794 3481 3.132160 TGACATGCCGTAAAGAAAACGA 58.868 40.909 0.00 0.00 42.90 3.85
2795 3482 3.529634 TGACATGCCGTAAAGAAAACG 57.470 42.857 0.00 0.00 40.01 3.60
2796 3483 7.462724 GCAATAATGACATGCCGTAAAGAAAAC 60.463 37.037 0.00 0.00 34.03 2.43
2797 3484 6.529829 GCAATAATGACATGCCGTAAAGAAAA 59.470 34.615 0.00 0.00 34.03 2.29
2806 3493 3.772932 ACAAAGCAATAATGACATGCCG 58.227 40.909 0.00 0.00 40.93 5.69
2809 3496 9.229784 GATGAACTACAAAGCAATAATGACATG 57.770 33.333 0.00 0.00 0.00 3.21
2825 3512 4.458989 GTCCCAAAAGCATGATGAACTACA 59.541 41.667 0.00 0.00 0.00 2.74
2843 3530 2.168106 GCATGCCATGTTAAATGTCCCA 59.832 45.455 6.36 0.00 0.00 4.37
2879 3566 1.798725 CGTGCAATTTCAGCCTGCG 60.799 57.895 0.00 0.00 38.97 5.18
2895 3582 2.124507 TAAGCCTTGCCTCTTGCCGT 62.125 55.000 0.00 0.00 40.16 5.68
3009 3696 2.621998 GCACCTATACTTCTCACCGCTA 59.378 50.000 0.00 0.00 0.00 4.26
3079 3766 6.700352 AGGCTTAAAATAACGGTGTACTACA 58.300 36.000 0.00 0.00 0.00 2.74
3264 3951 4.436050 CCATTCATGTTACTGCACTCGTTC 60.436 45.833 0.00 0.00 0.00 3.95
3265 3952 3.436704 CCATTCATGTTACTGCACTCGTT 59.563 43.478 0.00 0.00 0.00 3.85
3266 3953 3.002791 CCATTCATGTTACTGCACTCGT 58.997 45.455 0.00 0.00 0.00 4.18
3376 4067 5.521906 AGGGAAGAGAAAAGAAAAGCAAC 57.478 39.130 0.00 0.00 0.00 4.17
3429 4120 6.642707 AACAAAAATTTATCGACTGGGACA 57.357 33.333 0.00 0.00 0.00 4.02
3430 4121 6.584942 GGAAACAAAAATTTATCGACTGGGAC 59.415 38.462 0.00 0.00 0.00 4.46
3431 4122 6.265649 TGGAAACAAAAATTTATCGACTGGGA 59.734 34.615 0.00 0.00 37.44 4.37
3490 4181 7.375053 TCAGGGTCACTTGCAAATAATTAAAC 58.625 34.615 0.00 0.00 0.00 2.01
3502 4193 2.113860 TGCTAATCAGGGTCACTTGC 57.886 50.000 0.00 0.00 0.00 4.01
3505 4196 2.437281 CCAGATGCTAATCAGGGTCACT 59.563 50.000 0.00 0.00 36.15 3.41
3628 4319 6.043411 CCTCAGGTAAGTTATCACTAACAGC 58.957 44.000 0.00 0.00 39.81 4.40
3631 4322 6.127423 TGAGCCTCAGGTAAGTTATCACTAAC 60.127 42.308 0.00 0.00 37.99 2.34
3666 4357 1.339727 GCGGTCACTGGGGAAAGTTAT 60.340 52.381 0.00 0.00 0.00 1.89
3670 5765 2.359975 GGCGGTCACTGGGGAAAG 60.360 66.667 0.00 0.00 0.00 2.62


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.